Merge branch 'develop' into developtomchmmer

[jalview.git] / test / jalview / renderer / seqfeatures / FeatureColourFinderTest.java

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 7fd7abc..c0095fe 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -2,18 +2,20 @@ package jalview.renderer.seqfeatures;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotEquals;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.FeatureRenderer;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
 import java.awt.Color;
 import java.util.List;
@@ -41,7 +43,7 @@ import org.testng.annotations.Test;
  */
 public class FeatureColourFinderTest
 {
-  private AlignViewport av;
+  private AlignViewportI av;
 
   private SequenceI seq;
 
@@ -171,9 +173,9 @@ public class FeatureColourFinderTest
      * - currently no way other than mimicking reordering of
      * table in Feature Settings
      */
-    Object[][] data = new Object[2][];
-    data[0] = new Object[] { "Metal", red, true };
-    data[1] = new Object[] { "Domain", green, true };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[2];
+    data[0] = new FeatureSettingsBean("Metal", red, null, true);
+    data[1] = new FeatureSettingsBean("Domain", green, null, true);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.red);
@@ -181,7 +183,7 @@ public class FeatureColourFinderTest
     /*
      * ..and turn off display of Metal
      */
-    data[0][2] = false;
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.green);
@@ -215,8 +217,8 @@ public class FeatureColourFinderTest
     /*
      * turn off display of Metal - is this the easiest way to do it??
      */
-    Object[][] data = new Object[1][];
-    data[0] = new Object[] { "Metal", red, false };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.blue);
@@ -224,7 +226,7 @@ public class FeatureColourFinderTest
     /*
      * turn display of Metal back on
      */
-    data[0] = new Object[] { "Metal", red, true };
+    data[0] = new FeatureSettingsBean("Metal", red, null, true);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.red);
@@ -285,6 +287,28 @@ public class FeatureColourFinderTest
   }
 
   @Test(groups = "Functional")
+  public void testFindFeatureAtEnd()
+  {
+    /*
+     * terminal residue feature
+     */
+    seq.addSequenceFeature(new SequenceFeature("PDBRESNUM", "pdb res 1",
+            seq.getEnd(), seq.getEnd(), Float.NaN, "1seq.pdb"));
+    fr.setColour("PDBRESNUM", new FeatureColour(Color.red));
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+
+    /*
+     * final column should have PDBRESNUM feature, the others not
+     */
+    Color c = finder.findFeatureColour(Color.blue, seq,
+            seq.getLength() - 2);
+    assertNotEquals(c, Color.red);
+    c = finder.findFeatureColour(Color.blue, seq, seq.getLength() - 1);
+    assertEquals(c, Color.red);
+  }
+
+  @Test(groups = "Functional")
   public void testFindFeatureColour_graduatedFeatureColour()
   {
     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
@@ -299,7 +323,7 @@ public class FeatureColourFinderTest
      */
     Color min = new Color(100, 50, 150);
     Color max = new Color(200, 0, 100);
-    FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+    FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
     fr.setColour("kd", fc);
     fr.featuresAdded();
     av.setShowSequenceFeatures(true);
@@ -376,9 +400,9 @@ public class FeatureColourFinderTest
      * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
      * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
      */
-    Object[][] data = new Object[2][];
-    data[0] = new Object[] { "Metal", red, true };
-    data[1] = new Object[] { "Domain", green, true };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[2];
+    data[0] = new FeatureSettingsBean("Metal", red, null, true);
+    data[1] = new FeatureSettingsBean("Domain", green, null, true);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.cyan, seq, 10);
     assertEquals(c, new Color(153, 102, 41));
@@ -388,7 +412,7 @@ public class FeatureColourFinderTest
      * Domain (green) above background (pink)
      * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
      */
-    data[0][2] = false;
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.pink, seq, 10);
     assertEquals(c, new Color(102, 223, 70));
@@ -424,8 +448,8 @@ public class FeatureColourFinderTest
     /*
      * turn off display of Metal
      */
-    Object[][] data = new Object[1][];
-    data[0] = new Object[] { "Metal", red, false };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     assertTrue(finder.noFeaturesDisplayed());
 
@@ -469,7 +493,7 @@ public class FeatureColourFinderTest
      */
     Color min = new Color(100, 50, 150);
     Color max = new Color(200, 0, 100);
-    FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+    FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
     fc.setAboveThreshold(true);
     fc.setThreshold(5f);
     fr.setColour(kdFeature, fc);
@@ -480,9 +504,9 @@ public class FeatureColourFinderTest
     /*
      * render order is kd above Metal
      */
-    Object[][] data = new Object[2][];
-    data[0] = new Object[] { kdFeature, fc, true };
-    data[1] = new Object[] { metalFeature, green, true };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[2];
+    data[0] = new FeatureSettingsBean(kdFeature, fc, null, true);
+    data[1] = new FeatureSettingsBean(metalFeature, green, null, true);
     fr.setFeaturePriority(data);
 
     av.setShowSequenceFeatures(true);